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@@ -368,7 +368,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-intro-sce"><p>Content from <a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment class</a></p>
 <hr>
-<p>Last updated on 2024-10-04 |
+<p>Last updated on 2024-10-07 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -570,9 +570,14 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
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 </div>
 <p>Let’s look at an example dataset. <code>WTChimeraData</code> comes
-from a study on mouse development. We can assign one sample to a
-<code>SingleCellExperiment</code> object named <code>sce</code> like
-so:</p>
+from a study on mouse development <a href="https://www.nature.com/articles/s41586-019-0933-9" class="external-link">Pijuan-Sala et
+al.</a>. The study profiles the effect of a transcription factor TAL1
+and its influence on mouse development. Because mutations in this gene
+can cause severe developmental issues, Tal1-/- cells (positive for
+tdTomato, a fluorescent protein) were injected into wild-type
+blastocysts (tdTomato-), forming chimeric embryos.</p>
+<p>We can assign one sample to a <code>SingleCellExperiment</code>
+object named <code>sce</code> like so:</p>
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@@ -984,12 +989,19 @@ <h3 class="callout-title">Key Points</h3>
 </div>
 </div>
 </div>
+</div>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
+<hr class="half-width">
+<ol style="list-style-type: decimal">
+<li>Pijuan-Sala B, Griffiths JA, Guibentif C et al. (2019). A
+single-cell molecular map of mouse gastrulation and early organogenesis.
+Nature 566, 7745:490-495.</li>
+</ol>
 <!--
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use.
- -->
-</div>
-</section></section><section id="aio-eda_qc"><p>Content from <a href="eda_qc.html">Exploratory data analysis and quality control</a></p>
+ --></section></section><section id="aio-eda_qc"><p>Content from <a href="eda_qc.html">Exploratory data analysis and quality control</a></p>
 <hr>
 <p>Last updated on 2024-10-03 |
 
@@ -2744,7 +2756,7 @@ <h3 class="callout-title">Challenge</h3>
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   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -2941,7 +2953,7 @@ <h3 class="callout-title">Challenge</h3>
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+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
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 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3670,7 +3682,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
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 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
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 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -4151,7 +4163,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
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 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
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 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -4995,7 +5007,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
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 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -5009,7 +5021,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
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 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -5219,7 +5231,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-large_data"><p>Content from <a href="large_data.html">Working with large data</a></p>
 <hr>
-<p>Last updated on 2024-10-04 |
+<p>Last updated on 2024-10-07 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
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 </h3>
 <pre class="output" tabindex="0"><code>     approx
-exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   90   0   0   0   1   0   0   0   1   0   0   0   0   0   0
-   2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
-   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0  56
-   5    0   0   0   0 392   0   0   1   0   1   0   0   0   0   0
-   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
-   7    0   0   0   0   0 245   0   0   0   1   0   0   0   0   0
-   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
-   9    1   0   0   0   2   0   0   0 106   0   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 105   0   0   0   0   0
-   11   0   0   0   0   0   0   1   0   0   5 147   0   0   0   0
-   12   0   0   0   0   1   0   0   0   0  23   0 199   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0</code></pre>
+exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14
+   1   88   0   0   0   0   0   0   2   0   0   0   0   0   0
+   2    0  86   0   0   0   0   0   0   0   0   0   0   0   0
+   3    0  57  75   1   0   0   0   0   0   0   0   1   0   0
+   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0
+   5    0   0   0   0 176   0   0   0   0   0   0  11   0   0
+   6    0   0   0   0   0  73 128   0   0   1   0   0   0   0
+   7    0   0   0   0   0 253   0   0   1   0   0   0   0   0
+   8    1   0   0   0   0   0   0 106   0   0   0   1   0   0
+   9    0   0   0   0   0   0   0   0 113   0  10   0   0   0
+   10   0   0   0   0   0   0   0   0   0 153   0   0   0   0
+   11   0   0   0   0   0   0   0   0   0   0 198   0   0   0
+   12   0   0   0   0   0   0   0   0   1   0   0 312   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20
+   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
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 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -6247,7 +6260,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [131] spatstat.geom_3.2-9       RcppHNSW_0.6.0
 [133] reshape2_1.4.4            ScaledMatrix_1.12.0
 [135] BiocVersion_3.19.1        evaluate_0.23
-[137] renv_1.0.9                BiocManager_1.30.23
+[137] renv_1.0.10               BiocManager_1.30.23
 [139] httpuv_1.6.15             RANN_2.6.1
 [141] tidyr_1.3.1               purrr_1.0.2
 [143] polyclip_1.10-6           future_1.33.2
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 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
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 <p>Use the function <code>system.time</code> to obtain the runtime of
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 </div>
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-</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
-<hr class="half-width">
 <!--
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 any links that you are not going to use.
- --></section></section><section id="aio-hca"><p>Content from <a href="hca.html">Accessing data from the Human Cell Atlas (HCA)</a></p>
+ -->
+</section></section><section id="aio-hca"><p>Content from <a href="hca.html">Accessing data from the Human Cell Atlas (HCA)</a></p>
 <hr>
 <p>Last updated on 2024-10-04 |
 
@@ -6931,7 +6942,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
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diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index 2445313..1ec215c 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -516,7 +516,7 @@ <h3 class="callout-title">Challenge</h3>
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -710,7 +710,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
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-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
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+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1430,7 +1430,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
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@@ -1468,7 +1468,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</h3>
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 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
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@@ -1541,7 +1541,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
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 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -1575,7 +1575,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
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 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -1617,7 +1617,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
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-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
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 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
diff --git a/hca.html b/hca.html
index 37dfb6a..60cb06d 100644
--- a/hca.html
+++ b/hca.html
@@ -758,7 +758,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
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 </button>
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diff --git a/instructor/aio.html b/instructor/aio.html
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@@ -370,7 +370,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-intro-sce"><p>Content from <a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment class</a></p>
 <hr>
-<p>Last updated on 2024-10-04 |
+<p>Last updated on 2024-10-07 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
@@ -573,9 +573,14 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 </div>
 </div>
 <p>Let’s look at an example dataset. <code>WTChimeraData</code> comes
-from a study on mouse development. We can assign one sample to a
-<code>SingleCellExperiment</code> object named <code>sce</code> like
-so:</p>
+from a study on mouse development <a href="https://www.nature.com/articles/s41586-019-0933-9" class="external-link">Pijuan-Sala et
+al.</a>. The study profiles the effect of a transcription factor TAL1
+and its influence on mouse development. Because mutations in this gene
+can cause severe developmental issues, Tal1-/- cells (positive for
+tdTomato, a fluorescent protein) were injected into wild-type
+blastocysts (tdTomato-), forming chimeric embryos.</p>
+<p>We can assign one sample to a <code>SingleCellExperiment</code>
+object named <code>sce</code> like so:</p>
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@@ -987,12 +992,19 @@ <h3 class="callout-title">Key Points</h3>
 </div>
 </div>
 </div>
+</div>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
+<hr class="half-width">
+<ol style="list-style-type: decimal">
+<li>Pijuan-Sala B, Griffiths JA, Guibentif C et al. (2019). A
+single-cell molecular map of mouse gastrulation and early organogenesis.
+Nature 566, 7745:490-495.</li>
+</ol>
 <!--
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 any links that you are not going to use.
- -->
-</div>
-</section></section><section id="aio-eda_qc"><p>Content from <a href="eda_qc.html">Exploratory data analysis and quality control</a></p>
+ --></section></section><section id="aio-eda_qc"><p>Content from <a href="eda_qc.html">Exploratory data analysis and quality control</a></p>
 <hr>
 <p>Last updated on 2024-10-03 |
 
@@ -2749,7 +2761,7 @@ <h3 class="callout-title">Challenge</h3>
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -2946,7 +2958,7 @@ <h3 class="callout-title">Challenge</h3>
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -3244,7 +3256,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
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 <p>One important reason why is because averages over all other clusters
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 This example will set it to use four cores on your laptop, but you can
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 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
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 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
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 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
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 <p>After running the second pseudobulk DGE, you can join the two
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  -->
 </section></section><section id="aio-large_data"><p>Content from <a href="large_data.html">Working with large data</a></p>
 <hr>
-<p>Last updated on 2024-10-04 |
+<p>Last updated on 2024-10-07 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 12 minutes</p>
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 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
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 </h3>
 <pre class="output" tabindex="0"><code>     approx
-exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   90   0   0   0   1   0   0   0   1   0   0   0   0   0   0
-   2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
-   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0  56
-   5    0   0   0   0 392   0   0   1   0   1   0   0   0   0   0
-   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
-   7    0   0   0   0   0 245   0   0   0   1   0   0   0   0   0
-   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
-   9    1   0   0   0   2   0   0   0 106   0   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 105   0   0   0   0   0
-   11   0   0   0   0   0   0   1   0   0   5 147   0   0   0   0
-   12   0   0   0   0   1   0   0   0   0  23   0 199   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0</code></pre>
+exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14
+   1   88   0   0   0   0   0   0   2   0   0   0   0   0   0
+   2    0  86   0   0   0   0   0   0   0   0   0   0   0   0
+   3    0  57  75   1   0   0   0   0   0   0   0   1   0   0
+   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0
+   5    0   0   0   0 176   0   0   0   0   0   0  11   0   0
+   6    0   0   0   0   0  73 128   0   0   1   0   0   0   0
+   7    0   0   0   0   0 253   0   0   1   0   0   0   0   0
+   8    1   0   0   0   0   0   0 106   0   0   0   1   0   0
+   9    0   0   0   0   0   0   0   0 113   0  10   0   0   0
+   10   0   0   0   0   0   0   0   0   0 153   0   0   0   0
+   11   0   0   0   0   0   0   0   0   0   0 198   0   0   0
+   12   0   0   0   0   0   0   0   0   1   0   0 312   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20
+   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
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 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
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 [131] spatstat.geom_3.2-9       RcppHNSW_0.6.0
 [133] reshape2_1.4.4            ScaledMatrix_1.12.0
 [135] BiocVersion_3.19.1        evaluate_0.23
-[137] renv_1.0.9                BiocManager_1.30.23
+[137] renv_1.0.10               BiocManager_1.30.23
 [139] httpuv_1.6.15             RANN_2.6.1
 [141] tidyr_1.3.1               purrr_1.0.2
 [143] polyclip_1.10-6           future_1.33.2
@@ -6287,7 +6300,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
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 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
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 <p>Use the function <code>system.time</code> to obtain the runtime of
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-</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
-<hr class="half-width">
 <!--
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 any links that you are not going to use.
- --></section></section><section id="aio-hca"><p>Content from <a href="hca.html">Accessing data from the Human Cell Atlas (HCA)</a></p>
+ -->
+</section></section><section id="aio-hca"><p>Content from <a href="hca.html">Accessing data from the Human Cell Atlas (HCA)</a></p>
 <hr>
 <p>Last updated on 2024-10-04 |
 
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 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
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-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
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@@ -1415,7 +1415,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
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 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1432,7 +1432,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
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@@ -1470,7 +1470,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</h3>
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 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
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@@ -1543,7 +1543,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
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-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -1577,7 +1577,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
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+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -1619,7 +1619,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
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 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
diff --git a/instructor/hca.html b/instructor/hca.html
index 5a5b8ac..17c8632 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -760,7 +760,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
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-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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@@ -811,7 +811,7 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
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@@ -852,7 +852,7 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
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@@ -944,7 +944,7 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
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diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index 95b566a..5ad43ad 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -218,6 +218,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
       <div class="accordion-body">
         <ul><li><a href="#bioconductor">Bioconductor</a></li>
 <li><a href="#the-singlecellexperiment-class">The <code>SingleCellExperiment</code> class</a></li>
+<li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
 
@@ -327,7 +328,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to Bioconductor and the SingleCellExperiment class</h1>
-        <p>Last updated on 2024-10-04 |
+        <p>Last updated on 2024-10-07 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -521,9 +522,14 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 </div>
 </div>
 <p>Let’s look at an example dataset. <code>WTChimeraData</code> comes
-from a study on mouse development. We can assign one sample to a
-<code>SingleCellExperiment</code> object named <code>sce</code> like
-so:</p>
+from a study on mouse development <a href="https://www.nature.com/articles/s41586-019-0933-9" class="external-link">Pijuan-Sala et
+al.</a>. The study profiles the effect of a transcription factor TAL1
+and its influence on mouse development. Because mutations in this gene
+can cause severe developmental issues, Tal1-/- cells (positive for
+tdTomato, a fluorescent protein) were injected into wild-type
+blastocysts (tdTomato-), forming chimeric embryos.</p>
+<p>We can assign one sample to a <code>SingleCellExperiment</code>
+object named <code>sce</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
@@ -927,12 +933,15 @@ <h3 class="callout-title">Key Points</h3>
 </ul></div>
 </div>
 </div>
-<!--
+</div>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+<hr class="half-width"><ol style="list-style-type: decimal"><li>Pijuan-Sala B, Griffiths JA, Guibentif C et al. (2019). A
+single-cell molecular map of mouse gastrulation and early organogenesis.
+Nature 566, 7745:490-495.</li>
+</ol><!--
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use.
- -->
-</div>
-</section></div> <!-- / div.lesson-content -->
+ --></section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="../instructor/index.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="../instructor/eda_qc.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -990,7 +999,7 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-04",
+  "dateModified": "2024-10-07",
   "datePublished": "2024-10-07"
 }
 
diff --git a/instructor/large_data.html b/instructor/large_data.html
index c13098f..fbded44 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -259,7 +259,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#interoperability-with-popular-single-cell-analysis-ecosytems">Interoperability with popular single-cell analysis ecosytems</a></li>
 <li><a href="#session-info">Session Info</a></li>
 <li><a href="#exercises">Exercises</a></li>
-<li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
 
@@ -333,7 +332,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Working with large data</h1>
-        <p>Last updated on 2024-10-04 |
+        <p>Last updated on 2024-10-07 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -748,7 +747,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -818,21 +817,22 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="output" tabindex="0"><code>     approx
-exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   90   0   0   0   1   0   0   0   1   0   0   0   0   0   0
-   2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
-   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0  56
-   5    0   0   0   0 392   0   0   1   0   1   0   0   0   0   0
-   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
-   7    0   0   0   0   0 245   0   0   0   1   0   0   0   0   0
-   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
-   9    1   0   0   0   2   0   0   0 106   0   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 105   0   0   0   0   0
-   11   0   0   0   0   0   0   1   0   0   5 147   0   0   0   0
-   12   0   0   0   0   1   0   0   0   0  23   0 199   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0</code></pre>
+exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14
+   1   88   0   0   0   0   0   0   2   0   0   0   0   0   0
+   2    0  86   0   0   0   0   0   0   0   0   0   0   0   0
+   3    0  57  75   1   0   0   0   0   0   0   0   1   0   0
+   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0
+   5    0   0   0   0 176   0   0   0   0   0   0  11   0   0
+   6    0   0   0   0   0  73 128   0   0   1   0   0   0   0
+   7    0   0   0   0   0 253   0   0   1   0   0   0   0   0
+   8    1   0   0   0   0   0   0 106   0   0   0   1   0   0
+   9    0   0   0   0   0   0   0   0 113   0  10   0   0   0
+   10   0   0   0   0   0   0   0   0   0 153   0   0   0   0
+   11   0   0   0   0   0   0   0   0   0   0 198   0   0   0
+   12   0   0   0   0   0   0   0   0   1   0   0 312   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20
+   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -976,7 +976,7 @@ <h3 class="callout-title">Challenge</h3>
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -1348,7 +1348,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [131] spatstat.geom_3.2-9       RcppHNSW_0.6.0
 [133] reshape2_1.4.4            ScaledMatrix_1.12.0
 [135] BiocVersion_3.19.1        evaluate_0.23
-[137] renv_1.0.9                BiocManager_1.30.23
+[137] renv_1.0.10               BiocManager_1.30.23
 [139] httpuv_1.6.15             RANN_2.6.1
 [141] tidyr_1.3.1               purrr_1.0.2
 [143] polyclip_1.10-6           future_1.33.2
@@ -1379,7 +1379,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
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+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1393,7 +1393,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1485,7 +1485,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1547,11 +1547,11 @@ <h3 class="callout-title">Key Points</h3>
 </ul></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-<hr class="half-width"><!--
+<!--
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use.
- --></section></div> <!-- / div.lesson-content -->
+ -->
+</section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="../instructor/multi-sample.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="../instructor/hca.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -1609,7 +1609,7 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-04",
+  "dateModified": "2024-10-07",
   "datePublished": "2024-10-07"
 }
 
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index d5880b3..c6be40d 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -545,7 +545,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -608,7 +608,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -1057,7 +1057,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -1374,7 +1374,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -1388,7 +1388,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1423,7 +1423,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -1438,7 +1438,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1521,7 +1521,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
diff --git a/intro-sce.html b/intro-sce.html
index c5efb0e..22333f7 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -218,6 +218,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
       <div class="accordion-body">
         <ul><li><a href="#bioconductor">Bioconductor</a></li>
 <li><a href="#the-singlecellexperiment-class">The <code>SingleCellExperiment</code> class</a></li>
+<li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
 
@@ -327,7 +328,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to Bioconductor and the SingleCellExperiment class</h1>
-        <p>Last updated on 2024-10-04 |
+        <p>Last updated on 2024-10-07 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -519,9 +520,14 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 </div>
 </div>
 <p>Let’s look at an example dataset. <code>WTChimeraData</code> comes
-from a study on mouse development. We can assign one sample to a
-<code>SingleCellExperiment</code> object named <code>sce</code> like
-so:</p>
+from a study on mouse development <a href="https://www.nature.com/articles/s41586-019-0933-9" class="external-link">Pijuan-Sala et
+al.</a>. The study profiles the effect of a transcription factor TAL1
+and its influence on mouse development. Because mutations in this gene
+can cause severe developmental issues, Tal1-/- cells (positive for
+tdTomato, a fluorescent protein) were injected into wild-type
+blastocysts (tdTomato-), forming chimeric embryos.</p>
+<p>We can assign one sample to a <code>SingleCellExperiment</code>
+object named <code>sce</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
@@ -925,12 +931,15 @@ <h3 class="callout-title">Key Points</h3>
 </ul></div>
 </div>
 </div>
-<!--
+</div>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+<hr class="half-width"><ol style="list-style-type: decimal"><li>Pijuan-Sala B, Griffiths JA, Guibentif C et al. (2019). A
+single-cell molecular map of mouse gastrulation and early organogenesis.
+Nature 566, 7745:490-495.</li>
+</ol><!--
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use.
- -->
-</div>
-</section></div> <!-- / div.lesson-content -->
+ --></section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="index.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="eda_qc.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -988,7 +997,7 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-04",
+  "dateModified": "2024-10-07",
   "datePublished": "2024-10-07"
 }
 
diff --git a/large_data.html b/large_data.html
index a9bd7a2..961b156 100644
--- a/large_data.html
+++ b/large_data.html
@@ -259,7 +259,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#interoperability-with-popular-single-cell-analysis-ecosytems">Interoperability with popular single-cell analysis ecosytems</a></li>
 <li><a href="#session-info">Session Info</a></li>
 <li><a href="#exercises">Exercises</a></li>
-<li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
 
@@ -333,7 +332,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Working with large data</h1>
-        <p>Last updated on 2024-10-04 |
+        <p>Last updated on 2024-10-07 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -746,7 +745,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -816,21 +815,22 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="output" tabindex="0"><code>     approx
-exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   90   0   0   0   1   0   0   0   1   0   0   0   0   0   0
-   2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
-   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0  56
-   5    0   0   0   0 392   0   0   1   0   1   0   0   0   0   0
-   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
-   7    0   0   0   0   0 245   0   0   0   1   0   0   0   0   0
-   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
-   9    1   0   0   0   2   0   0   0 106   0   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 105   0   0   0   0   0
-   11   0   0   0   0   0   0   1   0   0   5 147   0   0   0   0
-   12   0   0   0   0   1   0   0   0   0  23   0 199   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0</code></pre>
+exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14
+   1   88   0   0   0   0   0   0   2   0   0   0   0   0   0
+   2    0  86   0   0   0   0   0   0   0   0   0   0   0   0
+   3    0  57  75   1   0   0   0   0   0   0   0   1   0   0
+   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0
+   5    0   0   0   0 176   0   0   0   0   0   0  11   0   0
+   6    0   0   0   0   0  73 128   0   0   1   0   0   0   0
+   7    0   0   0   0   0 253   0   0   1   0   0   0   0   0
+   8    1   0   0   0   0   0   0 106   0   0   0   1   0   0
+   9    0   0   0   0   0   0   0   0 113   0  10   0   0   0
+   10   0   0   0   0   0   0   0   0   0 153   0   0   0   0
+   11   0   0   0   0   0   0   0   0   0   0 198   0   0   0
+   12   0   0   0   0   0   0   0   0   1   0   0 312   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20
+   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -974,7 +974,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -1346,7 +1346,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [131] spatstat.geom_3.2-9       RcppHNSW_0.6.0
 [133] reshape2_1.4.4            ScaledMatrix_1.12.0
 [135] BiocVersion_3.19.1        evaluate_0.23
-[137] renv_1.0.9                BiocManager_1.30.23
+[137] renv_1.0.10               BiocManager_1.30.23
 [139] httpuv_1.6.15             RANN_2.6.1
 [141] tidyr_1.3.1               purrr_1.0.2
 [143] polyclip_1.10-6           future_1.33.2
@@ -1377,7 +1377,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1391,7 +1391,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1470,7 +1470,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1483,7 +1483,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1545,11 +1545,11 @@ <h3 class="callout-title">Key Points</h3>
 </ul></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-<hr class="half-width"><!--
+<!--
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use.
- --></section></div> <!-- / div.lesson-content -->
+ -->
+</section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="multi-sample.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="hca.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -1607,7 +1607,7 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-04",
+  "dateModified": "2024-10-07",
   "datePublished": "2024-10-07"
 }
 
diff --git a/md5sum.txt b/md5sum.txt
index 9de0485..6ed9b73 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -4,11 +4,11 @@
 "config.yaml" "b0d664d3d6abdd0e98b16282e1c03107" "site/built/config.yaml" "2024-09-24"
 "index.md" "1a5a4a9032969ed06a606ba9cba366b1" "site/built/index.md" "2024-10-04"
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-"episodes/intro-sce.Rmd" "bab83b985793d568bb9a6173d6080038" "site/built/intro-sce.md" "2024-10-04"
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diff --git a/multi-sample.html b/multi-sample.html
index e65d5b3..a0aeff2 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -543,7 +543,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -606,7 +606,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -1055,7 +1055,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -1372,7 +1372,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -1386,7 +1386,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1421,7 +1421,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -1436,7 +1436,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1519,7 +1519,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
diff --git a/pkgdown.yml b/pkgdown.yml
index 868ef4c..202a05d 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-10-07T17:27Z
+last_built: 2024-10-07T19:24Z